PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Araip.X9IXZ
Organism
Arachis ipaensis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Dalbergieae; Arachis
Family C2H2
Protein Properties Length: 1609aa    MW: 181993 Da    PI: 8.3992
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Araip.X9IXZgenomeNCGR_PGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.10.0006114941519123
                   EEET..TTTEEESSHHHHHHHHHH.T CS
      zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                   ++C    C++sF +k +L++H r+ +
  Araip.X9IXZ 1494 FQCDidGCTMSFGSKQELMHHKRNiC 1519
                   89********************9877 PP
2zf-C2H212.70.0003915191541323
                   ET..TTTEEESSHHHHHHHHHHT CS
      zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                   Cp   Cgk F ++ +L++H r+H
  Araip.X9IXZ 1519 CPvkGCGKKFFSHKYLVQHRRVH 1541
                   9999*****************99 PP
3zf-C2H211.70.0007915771603123
                   EEET..TTTEEESSHHHHHHHHHH..T CS
      zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                   y+C    Cg++F+  s++ rH r+  H
  Araip.X9IXZ 1577 YVCAepGCGQTFRFVSDFSRHKRKtgH 1603
                   899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.1E-151758IPR003349JmjN domain
PROSITE profilePS5118314.3541859IPR003349JmjN domain
PfamPF023753.4E-141952IPR003349JmjN domain
SuperFamilySSF511972.66E-25103134No hitNo description
SuperFamilySSF511972.66E-25189376No hitNo description
SMARTSM005582.2E-45192380IPR003347JmjC domain
PROSITE profilePS5118432.673192380IPR003347JmjC domain
PfamPF023735.3E-33225363IPR003347JmjC domain
Gene3DG3DSA:3.30.160.605.4E-414861516IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003559.114941516IPR015880Zinc finger, C2H2-like
SuperFamilySSF576676.86E-615171553No hitNo description
PROSITE profilePS5015712.50815171546IPR007087Zinc finger, C2H2
SMARTSM003550.004515171541IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.2E-515191545IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028015191541IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.603.8E-815461571IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001415471571IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.74115471576IPR007087Zinc finger, C2H2
PROSITE patternPS00028015491571IPR007087Zinc finger, C2H2
SuperFamilySSF576673.0E-915571601No hitNo description
Gene3DG3DSA:3.30.160.602.5E-915721600IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.26115771608IPR007087Zinc finger, C2H2
SMARTSM003550.6215771603IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028015791603IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009741Biological Processresponse to brassinosteroid
GO:0009826Biological Processunidimensional cell growth
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0033169Biological Processhistone H3-K9 demethylation
GO:0035067Biological Processnegative regulation of histone acetylation
GO:0040010Biological Processpositive regulation of growth rate
GO:0045815Biological Processpositive regulation of gene expression, epigenetic
GO:0048366Biological Processleaf development
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
GO:0071558Molecular Functionhistone demethylase activity (H3-K27 specific)
Sequence ? help Back to Top
Protein Sequence    Length: 1609 aa     Download sequence    Send to blast
MAEPNGDVFQ WLKSMPLAPE YRPTLTEFQD PIAYIFKIEK EASKYGICKI IPPFPPPPRK  60
VAIANFTRSL TKPDEPNSKP TFTTRQQQIG FCPRRPRPVQ RPVWQSGENY TFQEFEAKAK  120
AFEKSYLKKH HLHHQGHRKG GGAGGGSGGL GPLEVETLFW KATVDKPFSV EYANDMPGSA  180
FSRKCREECA AALAESAWNM REISRANGSL LRFMKEEIPG VTSPMVYLAM LFSWFAWHVE  240
DHDLHSLNYL HMGSGKTWYG VPRDAAVAFE DVVRVHGYGS EINPLGFGFT VNWFVEEHHW  300
VWIGVTFSTL GEKNTVMSPE VLINAGVPCC RLVQNAGEFV VTFPRAYHTG FSHGFNCGEA  360
ANIATPEWLR VAKDAAIRRA SVNHSPMVSH FQLLYDLALA LCSRFVFCYY GFLLFGYKKR  420
GEGETVIKEL FVQDVSQNND LLQELSKGSE IILLPRSSFD ISLCSKLRSG SKQRKVNSRF  480
SLGACNSEEM NSSKGFVSDD LAFSMNRGIK QEGSLSIKDK ITSLCERSMI SSYDVNGNIC  540
SSSSKPLQGD NERESGEGDG SPDKRLFSCV TCGILCFPCV AIVQPRESAA RYLMSADCSF  600
FNDWVVGSGV SSKKFIVHEE AAFPESRWTE KKTQNGLYQD PVQSAQYQLL TAERNYAESL  660
NSDRGKSNTA LALLASTYGN SSDSEEEQGD SDIVVDGHES PVINATLGGS PSNFQDACAI  720
PPTGPDSRND FSHQSFDHSL EKQDSDTASG LALKNMRAMY TNDTEKALLG KAMVPNDDKN  780
ASVIPQGDED SSRMHVFCLE HAVEAEQQLR PIGGAHIMLL CHPDFPKIEA EAKLVAEDLG  840
IDYLWKKIEY RHSSKEDEER IQVALDSEEA IPGNGDWCVK LGINLFYSST LSRSPLYSKQ  900
MPYNSVIYYA FGQSSPGSSP LEPKVYQRRV NKQKKIVAGK WCGKVWMSSQ VHPLLAKRDS  960
EDVEDEKSLH GWGLHDEKIE RSGSIPKSET SARKSGKKRK MTIENGRARK GSFAERDVDL  1020
DNPTEDKPNQ QLRRTLRSKQ ARDIESEGAD LEGDYSPPYH HRKPLSDQTN CTGSDAVSDD  1080
SLDDKFIDND VLSDDTMVYD SDCHQRFEHS SMQVEDIEDA VSEDSLDDSS LQLHRKNSKS  1140
KHARYIRKGR CIAEKEEMMS DDQLEPHKKK KQQRNPKSRQ AKYLAREDAI SHGQLEGHCR  1200
KYRKTPKGRL AKYVAGEDVS SDEQLENYSR KQQTSLPKRR KNKGVLTDDQ LEDHFQKQQK  1260
SVSRRRQNKG IERGVKDEMS DDQLEDHVQK QQTSVSRRRR NKQIEREDVM SDDEMEDHIQ  1320
KQRSSIPRNR QNSNSHLVHK TPKRKQAKCV DDDDGDDDDV NSDDEVEDDS QQKQQRTLRS  1380
KQSKPMTLKQ MKQARSLQMK NQTSRPVKRG AQTLKKLKAS QMRNKQSGKS REFSLKMEEG  1440
EEGGPSTRLR KRAPKVEESD GISKEKQTKK KRVKNATSAK AASNAKVKDE ENEFQCDIDG  1500
CTMSFGSKQE LMHHKRNICP VKGCGKKFFS HKYLVQHRRV HEDDRPLKCP WKGCKMTFKW  1560
AWARTEHIRV HTGARPYVCA EPGCGQTFRF VSDFSRHKRK TGHSTKKSR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A5e-7374014353Transcription factor jumonji (Jmj) family protein
6ip4_A5e-7374014353Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
114491471RKRAPKVEESDGISKEKQTKKKR
Functional Description ? help Back to Top
Source Description
UniProtHistone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3. Demethylates both tri- (H3K27me3) and di-methylated (H3K27me2) H3K27me (PubMed:21642989, PubMed:27111035). Demethylates also H3K4me3/2 and H3K36me3/2 in an in vitro assay (PubMed:20711170). Involved in the transcriptional regulation of hundreds of genes regulating developmental patterning and responses to various stimuli (PubMed:18467490). Binds DNA via its four zinc fingers in a sequence-specific manner, 5'-CTCTGYTY-3', to promote the demethylation of H3K27me3 and the regulation of organ boundary formation (PubMed:27111034, PubMed:27111035). Involved in the regulation of flowering time by repressing FLOWERING LOCUS C (FLC) expression (PubMed:15377760). Interacts with the NF-Y complexe to regulate SOC1 (PubMed:25105952). Mediates the recruitment of BRM to its target loci (PubMed:27111034). {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18467490, ECO:0000269|PubMed:20711170, ECO:0000269|PubMed:21642989, ECO:0000269|PubMed:25105952, ECO:0000269|PubMed:27111034, ECO:0000269|PubMed:27111035}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00608ChIP-seqTransfer from AT3G48430Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAraip.X9IXZ
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020975774.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A445AAM70.0A0A445AAM7_ARAHY; Uncharacterized protein
STRINGXP_007137965.10.0(Phaseolus vulgaris)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF56483250
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G48430.10.0relative of early flowering 6
Publications ? help Back to Top
  1. Li C, et al.
    Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 687-93
    [PMID:27111034]
  2. Cui X, et al.
    REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 694-9
    [PMID:27111035]
  3. Hyun Y, et al.
    Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem.
    Dev. Cell, 2016. 37(3): p. 254-66
    [PMID:27134142]
  4. Cheng JZ,Zhou YP,Lv TX,Xie CP,Tian CE
    Research progress on the autonomous flowering time pathway in Arabidopsis.
    Physiol Mol Biol Plants, 2017. 23(3): p. 477-485
    [PMID:28878488]
  5. Li C, et al.
    Verification of DNA motifs in Arabidopsis using CRISPR/Cas9-mediated mutagenesis.
    Plant Biotechnol. J., 2018. 16(8): p. 1446-1451
    [PMID:29331085]
  6. Wang X, et al.
    The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis.
    PLoS Genet., 2019. 15(4): p. e1008068
    [PMID:30969965]
  7. Qiu Q, et al.
    DNA methylation repels targeting of Arabidopsis REF6.
    Nat Commun, 2019. 10(1): p. 2063
    [PMID:31048693]